Variant report

Variant	rs2235432
Chromosome Location	chr22:29169420-29169421
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
2	chr22:29168270..29171327-chr22:29194850..29198169,6	MCF-7	breast:
3	chr22:29136431..29140671-chr22:29167494..29170117,5	K562	blood:
4	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
5	chr22:29168977..29169627-chr7:87505120..87506058,2	Hela-S3	cervix:
6	chr22:29167233..29170944-chr22:29195431..29200472,7	K562	blood:
7	chr22:29138183..29139139-chr22:29168668..29169506,2	Hela-S3	cervix:
8	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:
9	chr22:29135038..29141691-chr22:29167545..29172967,16	MCF-7	breast:
10	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
11	chr22:29134212..29140528-chr22:29167074..29172462,20	MCF-7	breast:
12	chr22:29167462..29171106-chr22:29208719..29213065,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000006634	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000272858	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000075303	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12168849	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2206061	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2294431	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997391	0.81[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs5997393	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997394	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997401	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6005856	0.84[ASN][1000 genomes]
rs6005857	0.87[ASN][1000 genomes]
rs6005866	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005868	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005877	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005899	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9625562	0.83[EUR][1000 genomes]
rs9625573	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9625575	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235432		cis	Lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29168200-29169600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr22:29168200-29169600	Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr22:29168200-29169600	Active TSS	K562	blood
4	chr22:29168200-29169800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr22:29168200-29169800	Active TSS	Brain Hippocampus Middle	brain
6	chr22:29168200-29169800	Active TSS	Rectal Smooth Muscle	rectum
7	chr22:29168200-29169800	Active TSS	Small Intestine	intestine
8	chr22:29168200-29169800	Active TSS	HSMMtube	muscle
9	chr22:29168200-29170000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:29168200-29170000	Active TSS	Right Atrium	heart
11	chr22:29168200-29170400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr22:29168200-29170600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr22:29168400-29169600	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr22:29168400-29169600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr22:29168400-29169600	Active TSS	Colon Smooth Muscle	Colon
16	chr22:29168400-29169600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr22:29168400-29169600	Active TSS	Fetal Kidney	kidney
18	chr22:29168400-29169600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr22:29168400-29169600	Active TSS	Fetal Lung	lung
20	chr22:29168400-29169800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr22:29168400-29169800	Active TSS	Colonic Mucosa	Colon
22	chr22:29168400-29169800	Active TSS	Fetal Muscle Trunk	muscle
23	chr22:29168400-29169800	Active TSS	Left Ventricle	heart
24	chr22:29168400-29169800	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr22:29168400-29169800	Active TSS	Stomach Mucosa	stomach
26	chr22:29168400-29169800	Active TSS	Thymus	Thymus
27	chr22:29168400-29170000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr22:29168400-29170000	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr22:29168400-29170000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr22:29168400-29170000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:29168400-29170000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr22:29168400-29170000	Active TSS	Brain Substantia Nigra	brain
33	chr22:29168400-29170000	Active TSS	Fetal Intestine Large	intestine
34	chr22:29168400-29170000	Active TSS	Fetal Intestine Small	intestine
35	chr22:29168400-29170000	Active TSS	Placenta	Placenta
36	chr22:29168400-29170000	Active TSS	Fetal Stomach	stomach
37	chr22:29168400-29170000	Active TSS	Ovary	ovary
38	chr22:29168400-29170000	Active TSS	Right Ventricle	heart
39	chr22:29168400-29170000	Active TSS	HMEC	breast
40	chr22:29168400-29170000	Active TSS	HSMM	muscle
41	chr22:29168400-29170200	Active TSS	H1 Cell Line	embryonic stem cell
42	chr22:29168400-29170200	Active TSS	A549	lung
43	chr22:29168400-29170200	Active TSS	NHDF-Ad	bronchial
44	chr22:29168400-29170200	Active TSS	NHLF	lung
45	chr22:29168400-29170400	Active TSS	GM12878-XiMat	blood
46	chr22:29168400-29170800	Active TSS	Psoas Muscle	Psoas
47	chr22:29168600-29169600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:29168600-29169600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:29168600-29169600	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr22:29168600-29169600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links